Thoughts in Between
by Shinto Red
Summary: A one shot that explores the moments not seen in during the final two episodes of Season 6.   Complete


**AN:** Hey everyone. This is my first Bones fic and frankly put my first fanfic in years. I had mostly come from the anime genre, but I got inspired by the season finally to write a little about what was not seen.

_Standard Disclaimer:_ I don't own the show, characters, etc. No personal profit gained. I'm just fulfilling my own guilty pleasure.

**Thoughts in Between**

By Shinto Red

The morning sun was peeking through the quiet bedroom of a certain FBI agent's apartment. The long narrow lines of light stretched from the edge of the bed, while it made its way in between the tangled sheets. The stream of light illuminated the smooth lower back of a sleeping anthropologist with chestnut colored hair. Her arms were slightly wrapped around a portion of blanket while she lay on her stomach. The morning light was clearly feeling puckish as it teased the dark haired agent lying beside her when it decided to gently reach further and highlight the curvature of her breast and the long, delicate fingers of her hand that was lighly beside it. He raised his dark brown eyes slowly as from the heels of her feet until they made their way to her face, where some strands of her hair were lightly strewn across it. Her soft rhythmic breathing would lightly push a few strands from her face before they landed once more on her skin. Booth raised his hand to brush the loose locks away, but decided against it at the last minute. She looked too peaceful to be disturbed.

His gaze lingered on her a moment longer before he let out a soft sigh and slowly tried to extricate himself from the bed. His slide his feet away from the warm and inviting blanket and lowered them gently to the dark hardwood floor of his bedroom. Goosebumps appeared on his skin as he slightly as a bit back a small groan when he started to push himself up. His head swung around suddenly and he let his body fall back when he felt warm, soft fingers on his wrist. Eyes the color of long faded blue jeans peered up at him in between the hair that he had been so tempted brush back behind her ear earlier. Though the fog of sleep was still present in her eyes, it was quickly being replaced with a multitude to of thoughts and emotions that were running far too fast to read until fear seemed to push itself forward as the dominant party, along with insecurity as its partner. She looked so lost…

Booth's heart constricted for a moment as he gave her a warm smile while he gently loosened the fingers on his wrist and raised the hand to his lips. He kissed each of her knuckles and that helped to ease the evident tension in her shoulders as her body seemed to meld with the bed and her head rested on the pillow once more. Booth slid back under the sheets and turned onto his side to face Brennan, all the while he maintained a hold on her hand. They were both tentatively looking at one another, neither entirely sure what step to take next.

"Booth?" she asked softly.

He raised her hand to his lips once again before letting it go. He then decided to indulge his earlier desire of brushing her hair behind her ear. "Yeah Bones?"

"Where were you going?"

"Just to shower… I'm sorry if I woke you up," he said as let his fingers lightly touch her bare shoulder.

Brennan looked down for a moment while her lips were tightly pressed in a straight line. She relaxed them slightly before looking up into Booth's chocolate pair. He knew what the question was before it rolled off her lips. "What… What are we?"

Booth closed his eyes and slowly released a breath before opening his eyes. "What do you think we are?"

A light frown crossed over Brennan's features. She was slightly irritated that Booth had answered her question with a question of his own. "Are you still angry?"

Booth shook his head. "Did you lose you imperviousness?"

Brennan looked thoughtful while she played with Booth's large coarse fingers. "I think so…"

"-Think?" Booth asked with an eyebrow raised in good humor.

Brennan flushed slightly as she looked down at their fingers once more. "It is a highly probable conclusion."

Booth leaned forward gave her nose a light peck as her eyes went wide with surprise. He gave her a small cheeky grin that lasted but a moment before the humor melted from his eyes as an intense look filtered through. "We crossed the line. Our red lines… There's no going back…"

"Then, we're a couple?" she asked softly.

He leaned in close to her face. His breath lightly tickling her as a small lopsided smile appeared on his face. "I guess we are."

Brennan hesitantly tilted her head to the side before closing the gap between them with a light chaste peck on Booths lips. A full grin spread across Booth's face, while he leaned in and gave her a soft, gentle kiss that started to drift to less than innocent levels. A heat was spreading across both their loins as the kiss deepened and Brennan's arms curled around Booth's neck. Booth groaned in mix of pleasure and frustration as he gently pushed himself away from her teasing and enticing warm body. He placed a final kiss behind her ear which caused Brennan to shiver slightly before he pulled away in a loose hug to meet her questioning gaze.

"As much as I would like to continue what we started, I have to go find Brodsky. Like you said last night… I need to hunt him down."

Brennan looked at him with concern. "I know this is illogical since it cannot be guaranteed… but…"

She surprised Booth by quickly enveloping him in a tight hug. "…Please, promise me you will take care of yourself."

"I will," he whispered into her ear. "I am not going to leave you. Not now. Not ever."

Her response was to hug him tighter.

* * *

><p>His right arm hung across her abdomen while she took note of the cracks in the ceiling of his bedroom. The light from a nearby streetlamp bathed the bed with its glow as the sun had done earlier. Brennan could hear Booth's soft and relaxed breathing by her ear. She had been earlier observing the defined bone structure of his face, while secretly wishing she could have continued down his chest which was covered by a black t-shirt. Angela would have certainly enjoyed that juicy little thought. Brennan smirked slightly though it disappeared quickly.<p>

The week had been nothing less than a rollercoaster, with all the highs, lows and corkscrews one could ever imagine in a case. Brennan could feel the sting of tears in her eyes as she tried to blink away the image in her mind of Vincent's life spreading around him in a deep crimson as Booth desperately triedto apply pressure at the location the bullet penetrated his chest. His desperate pleas begging that he stay were still ringing in her ears. From all the 'Squinterns,' as Booth called them, he had the greatest potential for success as a researcher. He had a deep passion for field and was clearly the most academically talented. He had creatively come up with the subject of the paper they were going to present at the conference during a mentoring session in limbo below the lab.

They had been examining a set of remains and somehow a reptilian specimen had been tossed into the mix of bones. The peculiarity had triggered one of his random fact dropping sessions about crocodiles being the modern day sample of ancient dinosaurs that quickly switched to him mentioning that the Jeffersonian had recently acquired a fine Tyrannosaurus Rex specimen for the newly remolded paleontology wing of the renowned institution.

"_I wonder what it would have been like to have lived at the time of such creatures?" he mused._

_Generally, Brennan would have brushed aside all topics of conversation that were not connected to the task at hand, but it was a slow afternoon and she decided to indulge the young doctoral student's thoughts. "Well, that is not physically possible since the spread of larger mammals, let along hominids, occurred at a far later stage in time. Furthermore, I am not certain that they could have survived the various climate changes such as the last ice age."_

_A small look of surprise passed over his features due to his mentor's sudden interest in continuing the topic. He cleared his throat and decided to seize this rare opportunity. "Yes, that is clear, Dr. Brennan. I was just humoring myself. I am not sure in any scenario though that I, as a mere mortal, would have stood a chance against such a titan, even if it was reduced to my height."_

_He caught a glint in his supervisor's eyes and one could almost see the wheels in her head as a thoughtful look spread across her delicate features. "What if we tested that?"_

"_What are you suggesting, Dr. Brennan?_

"_What if we calculated a potential confrontation between the two?"_

_Vincent's blue eyes twinkled with excitement. "Perhaps we could use a region specific test of strength… I believe a perfect example would be colloquially known as 'arm wrestling.'"_

_Brennan gave her young intern a smile. "You know, as a doctoral student it is important to be published in academic journals or to at least present research material at a conference… Mr. Nigel-Murray, how would you feel about conducting a joint collaboration for the upcoming anthropological conference that will be held here at the Jeffersonian?"_

"_I think it would be lovely, Dr. Brennan."_

"_Well, it was your idea… I also think it would be appropriate that your name appear first on the title."_

_He seemed to have lost his ability to speak for a second. "Th-Thank you, Dr. Brennan." _

_An almost wicked grin appeared on her face. "At least this conference will not be completely dry with the Neanderthal specialists taking over as it was the case last time…"_

_Vincent chuckled and smiled at her comment._

Brennan smiled warmly at the memory that had unfortunately become bitter-sweet. Little did either of them know that this would be one their last interactions. Brennan swallowed the lump that started to form in her throat and let out a ragged breath. It was not fair that someone so young and full of potential should expire. A cold chill spread across her body when she thought of who the original target was supposed to have been. She turned once more to observe his ruffed jawline. The case had been a stressful and high intensity. Few cases forced the Jeffersonian team to work at maximum capacity. It felt like Brennan had been holding her breath the entire time Booth had gone to hunt down Brodsky until she received a phone call confirming his success. The relief that washed over her was slightly mingled with embarrassment when Angela gave her knowing looks from across the room.

Angela… she had grown to love her sassy friend to the point that she had become the sister that she never had. Though she did not mind 'dishing,' as Angela called it, on her sexual exploits; when it came to Booth… she was suddenly reserved. A smile spread across her face when she recalled just how startled she was with Angela's response to her coy smile and Hodgin's poor timing. Her insistence on receiving _all _the details of that night made the experience almost feel like one of the interrogations she and Booth conducted on a suspect.

_Brennan's eyes were still lingering where Hodgins had just stood only moments before. "Bren?"_

_She blinked in surprise and turned to Angela. "Details. Now."_

_Brennan looked down once more with a small shy smile curling her lips. She could feel a hint of color filling her cheeks. "It was… unexpected, but it easily matched up to expectations."_

_A smirk formed on Angela's face. "In other words it was as hot as one of your Kathy and Andy encounters."_

_Brennan's eyes shot up to look at her. "…An…Ange…!"_

"_I knew it! There is no way that over six years of pent up sexual tension could be anything less than mind blowing."_

_Brennan could not believe her blush could get any deeper until she felt the tips of her ears burn. She suddenly felt Angela's arms around her as she looked up in surprise. "Oh Bren, I'm so happy for you… both of you… You both deserve a chance at happiness."_

_She lightly pulled away from her hug and gave her a small smile._

She shook her head. She made her best friend swear an oath of secrecy about the change in her relationship status, which she readily agreed to so that they could 'have their honeymoon period.' Brennan recalled how she frowned at that comment and was about to correct Angela… Though in some ways, she was not completely incorrect. The period of time following the union of spouses was used to ensure that the next generation would be sired…

Brennan's knuckles turned white while she held unto to the bedding in a death grip. The night had been wonderful and 'mind blowing' as her best friend phrased it, despite all the sorrow. But it also symbolized a level of stupidity she had never experienced with her prior sexual encounters. Brennan always prided herself on her rationality and intelligence. She always made sure to use both oral and barrier methods of contraception, especially with new partners, while at the same time being on top of her health care in that matter. Unfortunately, her regular oral contraceptive suddenly started to give her undesirable side effects prior to the expedition to Maluku. She was forced to stop consuming them. Since she was neither sexually active at the time, nor did she have an interest to pursue a sexual relationship while digging for the origins of man, she was not in any rush to experiment with a new pill. As a precaution, she packed a supply of barrier method contraception in her bag. Better to be safe than sorry… That idea went flying out the door that night with Booth though…

She was emotional and she let herself fall in the moment after that first tentative kiss to the heat that boiled over after. And, she had potentially exposed herself to very complicated situation – the creation of new life. She had unfortunately only realized this detail after Brodsky had been captured. Far too much time passed by then for her to even utilize potential emergency contraception, which she unsure if that was a blessing in disguise. She would only know with more certainty of an increased probability that she had conceived once the date of her coming menstrual cycle would arrive. She theoretically could try to do a blood test on herself at the lab, but there was still a potential for a false positive and she did not care for the unwanted eyes of her colleagues. By the time she would be able to schedule a test with her gynecologist, she could just as well conduct the test with the consumer versions found on the market. The former would just be used as a confirmation or negation of the results.

Even with the dry facts running through her mind while she logically tried to dissect the situation, she could not ease the palpations her heart was exerting and her parched throat. Her breathing increased in pace and she squeezed her eyes shut. She was desperately trying to gain control once again to prevent hyperventilation. They had only just started to enjoy this new level of intimacy.

"Why did things always have to be complicated for us?" she breathed out loud.

* * *

><p>The next few weeks appeared to pass by in relative calm. Brennan decided to utilize this time to tie up loose ends in her academic interests. The Jefferesonian had reverted back to the quiet of a more traditional research institution where everyone mostly kept to themselves in their offices. Angela's expected due date had come and gone and which had made her more than a little frustrated as she waddled into Brennan's office.<p>

"Hey Bren. Do you have some time?"

Brennan looked up from the journal article she was preparing for publication. "Ange, are you experiencing contractions?"

Angela shook her head with her long locks swishing lightly from side to side. She let out a sigh. "No, I wish… that's what I wanted to talk to you about… I need to vent to someone other than Jack."

Brennan nodded and got up from behind her desk while Angela eased herself down on the couch. "This kid is terrible. I think they could become the next David Beckham with what the little one is doing to my bladder. Seems like the baby is also experiencing cabin fever and wants to get out."

Brennan gave her a quizzical look. "I've never heard of any medical condition called 'cabin fever.'"

Angela gave her a look and understanding flashed in Brennan's eyes. "You were using an expression."

"Yes…"

Brennan cocked her head to the side. "Well, your current delay is not an irregular occurrence. If needed, the doctors will induce labor."

" Yeah…" Angela said with a sigh. "I know… I am just still hoping it will go naturally. All I know is that the both of us want the little guy out already…"

"I think it would probably be especially helpful for Hodgins and his blood pressure.." Brennan mused.

"Tell me about it. I just say 'hi' and he's running around like a chicken with its head cut off trying to find his car keys' thinking it means it's go time."

"It would also improve lab safety…" Brennan noted thinking back to one experience knocked over all the measuring tools that were being used by Brennan and Wendell to examine a soldier from WWII.

Angela chuckled. "Enough about me… how's it going with you and the FBI stud?"

Brennan gave her a small smile. "Good."

"Oh sweetie, you know you can ease up with all the details…" said Angela dryly.

She had a grin on face and she just shook her head when Brennan gave her a confused look. "Bren, what have you two been up to?"

"Oh… we have mostly been staying at either his apartment or mine. Watching Booth's television, having discussions-"

"-And hot sex."

Brennan shot Angela a look even though her ears were burning. "It must really be good – you are never shy talking about this type of stuff with anyone."

"Ange…" she said in a low warning tone.

"Sorry, but it's gotten problematic on my end to enjoy that activity," Angela responded with a cheeky grin and a wink. "I was wondering, but were you two at the park the other day…?"

Brennan took a second to recall the evening stroll she took with Booth two days ago. "Yes, we were out on Tuesday evening to get some fresh air. Why?"

"So I was right. I saw you two in the distance, holding hands… being so romantic," said Angela with a dramatic wistful sigh as she caught the glare Brennan sent her. "Hey, you should be thankful. I distracted Jack by sending him off to a vender to buy me a sandwich until you guys-"

Brennan's mobile phone rang suddenly and she caught a glimpse of her partner's name across the screen. "Hey Bones. We got a case."

* * *

><p>'Are we so blatant?' she thought to herself.<p>

She was sitting in the passenger side of Booth's government issue SUV. It was the day of the operation and they were going to pick up her father so that they could go to the bowling alley.

"What are you thinking about Bones?" asked Booth while wearing his ridiculous mullet and trucker's cap.

"Are we… can it be seen that something changed?" she asked and pressed her lips together.

Booth briefly glanced at her with an unreadable expression. "Why does it bother you?"

Brennan sighed. She could see Booth's jaw was slightly clenched and she gently placed a hand on his shoulder. "I…I really enjoy what has been developing between the two of us."

Brennan could feel the tension in his muscles underneath his bowling shirt. "Booth… Booth I have not exactly experienced this level of intimacy with anyone… and I… you know that I don't divulge necessarily that many details regarding myself… What I'm trying to explain is that… What goes on between us… that should just be ours…"

Booth's shoulder dropped slightly and he let out a slow breath before a slow smile curled on his lips. "That sounds familiar."

She let out a breath she was not she had been holding as well. "You're dad got you nervous, huh?"

"Well, that's your fault."

Booth's eyebrow shot up, though he had a smirk on his lips. "My fault?"

"You should not have said that I was playing your girlfriend without some warning… My father clearly noticed my hesitation after the statement you made."

Booth did not know whether to laugh or get irritated. "Bones, you are unbelievable."

"Why?"

Booth just shook his head with a smile. He pulled the vehicle in front of Max's residence. Brennan was still looking intently at him waiting for a response. Instead, Booth turned to her and gave her a light peck on the lips before opening the door to the car. Inside, a flushed faced anthropologist was left confused and lost in her thoughts until a light tapping on the window shook her out of her trance and she went outside to pick up her father.

* * *

><p>Booth's knee was bouncing up and down as he rotate his shoulders to ease the discomfort he was experiencing while sitting in the hard plastic hospital bench. They had received notification that Angela had gone into labor while they were undercover at the bowling alley. Though he did not want to admit it, he was also unnerved by Max's perceptiveness. He knew that he figured out that they were a couple; especially after the flirty and affectionate kiss on the cheek he gave Brennan when Max insisted that they 'act like a couple.' He let out a sigh and briefly glanced at her to his side. Though it appeared as if she was staring intently at Angela's door, she was clearly lost in thought. Her eyebrows were lightly furrowed and she was fiddling lightly with the white rabbit's ears in her lap. The pair had purchased the soft bundle at the hospital gift upon their arrival.<p>

There was something off about her. Clearly she was experiencing anxiety, but he just took it as worry for her friend. A muffled shriek came through the dull off-white door and Booth could only wince at the sound. 'I am so happy to be a guy…'

He caught something glittering out of the corner of his eye and he noticed Brennan's ring that her mother left her. A grin was tugging at the corners of his mouth as he recalled with pleasure how Brennan, unlike their Las Vegas undercover experience, she had stated that they were engaged. Booth chuckled and muttered to himself what she had said previously when they were in Sin City as Roxy. "Engaged to be engaged…"

"Booth? Did you say something?"

Booth lightly shook his head and focused on her pale blue eyes. Though he tried to mask it, a light blush colored his cheeks. "Um… do you want coffee?"

She shook her head and he got up to find a machine so as not to arouse her suspicions. Booth pulled out the changed from his pocket and popped the coins into the machine before pressing his preference. A cup dropped and soon after the steaming dark brown liquid was poured into it. Booth gently eased the steaming container from the machine and cradled it in his hands as he walked back to his partner and took a seat perpendicular to her in the drab waiting room. Suddenly the door opened and a beaming Hodgins stepped out with a light blue bundle in his arms. Booth felt a wave of nostalgia flood through him as he recalled cradling his own son when he was born. The Jeffersonian team crowded around the newborn and the proud new father. Brennan gave Booth a brief look that he could not exactly read before she focused on the newborn once again. She gave a small smile and then walked into the other room to see the exhausted new mother.

* * *

><p>Brennan had her fists stuffed into her trenchcoat's pockets. She appeared to be intently focused on the sidewalk while they made their way from the hospital to Booth's vehicle. The dark haired FBI agent tried to hide his frown as he would sneak peeks at her from the corner of his eyes. He did understand the cause of the deep creases of concentration and concern on her forehead. She suddenly pulled her hands out of her pockets and let them swing in the natural pattern. She suddenly shifted her head to her right face Booth.<p>

"They looked so happy."

Booth was slightly surprised to hear her suddenly speak. He briefly glanced at her once more with a look that was a mix of curiosity and concern for his partner before responding. "Well, yeah, they had a baby."

As the conversation between progressed he nodded his head in understanding to himself as he stopped in front her. 'She must be worried about Angela's baby…'

He continued to explain why everything was fine for the new Hodgins' family and how this was the happiest day of their lives. Yet, Brennan continued to look at him, trying to convey something with pale blue eyes that he was unable to decipher to for once. "What?"

She opened her mouth and closed it before the words came stumbling out. "I'm… I'm pregnant."

Booth's face went slack and his mind was blank. The wind felt like it had been knocked out of him.

"You're the father," she said as she briefly pursed her lips and her eyes filled with anxiety.

His mind and his hearing slowly connected. His heart soon started to swell with joy so great that only the birth of his son could match it. A smile slowly spread across his face and he let out laugh that was practically a gasp. He saw his partner let out a small, nervous laugh as she quickly mirrored his happiness with large smile of her own. "A baby… Our baby!"

* * *

><p><em><strong>And that's it folks. I'm not feeling creative enough to go further. There are more than enough authors right now filling that void and I generally would like to hold off on my own speculations and wait and see what the show will present in the fall. Not sure I will write anything further for this fandom, but I nevertheless enjoyed this writing exercise and hope you did as well. <strong>_


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